Langevin and Navier–Stokes simulation of three-dimensional protoplasmic streaming
International audience In this paper, we report the numerical results obtained using the Langevin Navier-Stokes (LNS) simulation of the velocity distribution of three-dimensional (3D) protoplasmic streaming in plant cells, such as those of Nitella flexilis. The LNS simulations are performed on 3D cy...
Published in: | Physica A: Statistical Mechanics and its Applications |
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Online Access: | https://hal.science/hal-04399527 https://hal.science/hal-04399527/document https://hal.science/hal-04399527/file/PHYSA-231496-R2.pdf https://doi.org/10.1016/j.physa.2023.129154 |
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ftccsdartic:oai:HAL:hal-04399527v1 2024-02-27T08:43:07+00:00 Langevin and Navier–Stokes simulation of three-dimensional protoplasmic streaming Noro, Shuta Hongo, Satoshi Nagahiro, Shin-Ichiro Ikai, Hisatoshi Koibuchi, Hiroshi Nakayama, Madoka Uchimoto, Tetsuya Diguet, Gildas National Institute of Technology (KOSEN) Hokkaido University Sapporo, Japan Institute of Fluid Sciences Sendai (IFS) Tohoku University Sendai ELyTMaX École Centrale de Lyon (ECL) Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL) Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon) Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Tohoku University Sendai -Centre National de la Recherche Scientifique (CNRS) 2023-10 https://hal.science/hal-04399527 https://hal.science/hal-04399527/document https://hal.science/hal-04399527/file/PHYSA-231496-R2.pdf https://doi.org/10.1016/j.physa.2023.129154 en eng HAL CCSD Elsevier info:eu-repo/semantics/altIdentifier/arxiv/2112.13460 info:eu-repo/semantics/altIdentifier/doi/10.1016/j.physa.2023.129154 hal-04399527 https://hal.science/hal-04399527 https://hal.science/hal-04399527/document https://hal.science/hal-04399527/file/PHYSA-231496-R2.pdf ARXIV: 2112.13460 doi:10.1016/j.physa.2023.129154 info:eu-repo/semantics/OpenAccess ISSN: 0378-4371 EISSN: 0378-4371 Physica A: Statistical Mechanics and its Applications https://hal.science/hal-04399527 Physica A: Statistical Mechanics and its Applications, 2023, 628, pp.129154. ⟨10.1016/j.physa.2023.129154⟩ Langevin simulations Brownian motion Navier-Stokes Fluctuation-dissipation relation Protoplasmic streaming Velocity distribution [PHYS.MPHY]Physics [physics]/Mathematical Physics [math-ph] info:eu-repo/semantics/article Journal articles 2023 ftccsdartic https://doi.org/10.1016/j.physa.2023.129154 2024-01-28T00:02:05Z International audience In this paper, we report the numerical results obtained using the Langevin Navier-Stokes (LNS) simulation of the velocity distribution of three-dimensional (3D) protoplasmic streaming in plant cells, such as those of Nitella flexilis. The LNS simulations are performed on 3D cylinders discretized by regular cubes in which fluid velocities are activated by boundary velocities parallel and nonparallel to the longitudinal direction and a random Brownian force with strength D. We find that, for a finite D, the velocity distribution h(V), V = | ⃗ V |, has two different peaks at a small non-zero V and a finite V , and the distribution h(V z) for |V z | along the longitudinal direction also has a peak at finite V z. These results are in good agreement with the reported velocity distributions observed using laser Doppler velocimetry. Moreover, we study the effects of the Brownian force on biological material mixing and find that mixing along the ⃗ V direction enhanced by the nonparallel circular motion is further improved by the Brownian force in the experimentally relevant region of D. In addition, the experimentally relevant D is found to be consistent with the expectation from the fluctuation dissipation relation between the random stress and viscosity in the LNS equation of Landau and Lifschitz for incompressible fluids. Article in Journal/Newspaper Nitella flexilis Archive ouverte HAL (Hyper Article en Ligne, CCSD - Centre pour la Communication Scientifique Directe) Physica A: Statistical Mechanics and its Applications 628 129154 |
institution |
Open Polar |
collection |
Archive ouverte HAL (Hyper Article en Ligne, CCSD - Centre pour la Communication Scientifique Directe) |
op_collection_id |
ftccsdartic |
language |
English |
topic |
Langevin simulations Brownian motion Navier-Stokes Fluctuation-dissipation relation Protoplasmic streaming Velocity distribution [PHYS.MPHY]Physics [physics]/Mathematical Physics [math-ph] |
spellingShingle |
Langevin simulations Brownian motion Navier-Stokes Fluctuation-dissipation relation Protoplasmic streaming Velocity distribution [PHYS.MPHY]Physics [physics]/Mathematical Physics [math-ph] Noro, Shuta Hongo, Satoshi Nagahiro, Shin-Ichiro Ikai, Hisatoshi Koibuchi, Hiroshi Nakayama, Madoka Uchimoto, Tetsuya Diguet, Gildas Langevin and Navier–Stokes simulation of three-dimensional protoplasmic streaming |
topic_facet |
Langevin simulations Brownian motion Navier-Stokes Fluctuation-dissipation relation Protoplasmic streaming Velocity distribution [PHYS.MPHY]Physics [physics]/Mathematical Physics [math-ph] |
description |
International audience In this paper, we report the numerical results obtained using the Langevin Navier-Stokes (LNS) simulation of the velocity distribution of three-dimensional (3D) protoplasmic streaming in plant cells, such as those of Nitella flexilis. The LNS simulations are performed on 3D cylinders discretized by regular cubes in which fluid velocities are activated by boundary velocities parallel and nonparallel to the longitudinal direction and a random Brownian force with strength D. We find that, for a finite D, the velocity distribution h(V), V = | ⃗ V |, has two different peaks at a small non-zero V and a finite V , and the distribution h(V z) for |V z | along the longitudinal direction also has a peak at finite V z. These results are in good agreement with the reported velocity distributions observed using laser Doppler velocimetry. Moreover, we study the effects of the Brownian force on biological material mixing and find that mixing along the ⃗ V direction enhanced by the nonparallel circular motion is further improved by the Brownian force in the experimentally relevant region of D. In addition, the experimentally relevant D is found to be consistent with the expectation from the fluctuation dissipation relation between the random stress and viscosity in the LNS equation of Landau and Lifschitz for incompressible fluids. |
author2 |
National Institute of Technology (KOSEN) Hokkaido University Sapporo, Japan Institute of Fluid Sciences Sendai (IFS) Tohoku University Sendai ELyTMaX École Centrale de Lyon (ECL) Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL) Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon) Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Tohoku University Sendai -Centre National de la Recherche Scientifique (CNRS) |
format |
Article in Journal/Newspaper |
author |
Noro, Shuta Hongo, Satoshi Nagahiro, Shin-Ichiro Ikai, Hisatoshi Koibuchi, Hiroshi Nakayama, Madoka Uchimoto, Tetsuya Diguet, Gildas |
author_facet |
Noro, Shuta Hongo, Satoshi Nagahiro, Shin-Ichiro Ikai, Hisatoshi Koibuchi, Hiroshi Nakayama, Madoka Uchimoto, Tetsuya Diguet, Gildas |
author_sort |
Noro, Shuta |
title |
Langevin and Navier–Stokes simulation of three-dimensional protoplasmic streaming |
title_short |
Langevin and Navier–Stokes simulation of three-dimensional protoplasmic streaming |
title_full |
Langevin and Navier–Stokes simulation of three-dimensional protoplasmic streaming |
title_fullStr |
Langevin and Navier–Stokes simulation of three-dimensional protoplasmic streaming |
title_full_unstemmed |
Langevin and Navier–Stokes simulation of three-dimensional protoplasmic streaming |
title_sort |
langevin and navier–stokes simulation of three-dimensional protoplasmic streaming |
publisher |
HAL CCSD |
publishDate |
2023 |
url |
https://hal.science/hal-04399527 https://hal.science/hal-04399527/document https://hal.science/hal-04399527/file/PHYSA-231496-R2.pdf https://doi.org/10.1016/j.physa.2023.129154 |
genre |
Nitella flexilis |
genre_facet |
Nitella flexilis |
op_source |
ISSN: 0378-4371 EISSN: 0378-4371 Physica A: Statistical Mechanics and its Applications https://hal.science/hal-04399527 Physica A: Statistical Mechanics and its Applications, 2023, 628, pp.129154. ⟨10.1016/j.physa.2023.129154⟩ |
op_relation |
info:eu-repo/semantics/altIdentifier/arxiv/2112.13460 info:eu-repo/semantics/altIdentifier/doi/10.1016/j.physa.2023.129154 hal-04399527 https://hal.science/hal-04399527 https://hal.science/hal-04399527/document https://hal.science/hal-04399527/file/PHYSA-231496-R2.pdf ARXIV: 2112.13460 doi:10.1016/j.physa.2023.129154 |
op_rights |
info:eu-repo/semantics/OpenAccess |
op_doi |
https://doi.org/10.1016/j.physa.2023.129154 |
container_title |
Physica A: Statistical Mechanics and its Applications |
container_volume |
628 |
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129154 |
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